We have just sequenced the whole genome of a bacteria. We aim to detect if any recombinant gene is inserted into the genome. Inserted gene is unknown.
- Mapped the paired-reads to our organism reference genome. (via bwa)
- Extracted the unmapped paired reads. (both pairs shouldn't be mapped) (via samtools)
- Performed de novo assembly with those unmapped reads. (via velvet)
Now, I have ~400 contigs and I'll BLAST each of them. Is it a valid approach?
Or should I focus on another method? Maybe I should focus on integration breakpoints instead of unmapped reads?